_pkgdown.yml

navbar:
  left:
  - icon: fa-home fa-lg
    href: index.html
  - text: Reference
    href: reference/index.html
  - text: Articles
    menu:
      - text: "Using the incidence package"
      - text: "Overview"
        href: articles/overview.html
      - text: "Customising Epicurves (visualisation)"
        href: articles/customize_plot.html
      - text: "Exporting Incidence Data"
        href: articles/conversions.html
      - text: "------------------"
      - text: "Understanding the incidence package"
      - text: "The incidence class (data)"
        href: articles/incidence_class.html
      - text: "The incidence_fit class (models)"
        href: articles/incidence_fit_class.html
  - text: Changelog
    href: news/index.html
  right:
  - icon: fa-github fa-lg
    href: https://github.com/reconhub/incidence

reference:
- title: Data Conversion
  desc: > 
    Functions for computing and converting incidence objects
  contents:
  - '`incidence`'
  - '`as.data.frame.incidence`'
- title: Incidence Curve Visualisation
  desc: >
    Functions for plotting incidence curves and models
  contents:
  - '`plot.incidence`'
  - '`incidence_pal1`'
- title: Accessors
  desc: Accessor functions for the incidence object
  contents:
  - '`get_counts`'
  - '`get_dates`'
  - '`get_fit`'
  - '`group_names`'
  - '`dim.incidence`'
- title: Data Manipulation
  desc: >
    Functions for manipulating incidence objects by date or group
  contents:
  - '`subset.incidence`'
  - '`pool`'
  - '`cumulate`'
- title: Parameter Estimation
  desc: > 
    Functions for estimating parameters such as peak and doubling time
  contents:
  - '`bootstrap`'
  - '`estimate_peak`'
  - '`find_peak`'
  - '`fit`'